PHOTOELECTRON-SPECTRA OF VARIOUS CORE LEVELS IN SOME RARE-EARTH N-ACETYLVALINE BIOINORGANIC COMPLEXES

X-ray photoelectron spectra of some bioinorganic complexes of La, Pr, Nd, Sm, and Gd with N-acetylvaline have-been measured. The complex formation does not give any detectable influence on the binding energy of the N 1s peak in the amino group, but has some appreciable effect on the binding energy of the C 1s peak and the O 1s peak in the carboxyl and carbonyl group of the biological ligand. The spin-orbit splitting between the 3d5/2 and 3d3/2 core level of the rare earth ion in these bioinorganic complexes also becomes slightly larger than that of the free rare earth atom due to the effect of the crystal field from the biological ligands.

ELECTRONIC-STRUCTURE AND CHEMICAL BONDING OF EUROPIUM NITRATE COMPLEX WITH AZACROWN (2, 2)

The electronic structure and bond character of europium nitrate complex with azacrown (2, 2)(1, 7, 10, 16-tetraoxa-4, 13-diazacyclooctadecane), [Eu(NO_3)_2(2, 2)] NO_3, have been studied by means of XPS and INDO method. The data of electronic binding energies and charge distribution of atoms in the complex showed that chemical shift of less electronegative nitrogen N1s binding energy was larger than that of more electronegative oxygen O1s binding energy in coordinating atoms, and that charge transfer from N...

Theoretical study on adsorption of Na+ and Na+(H2O)(n) (n=1-6) on a clean Si(111) surface

To model the adsorption of Na+ in aqueous solution on the semiconductor surface, the interactions of Na+ and Na+(H2O)(n) (n = 1-6) with a clean Si(111) surface were investigated by using hybrid density functional theory (B3LYP) and Moller-Plesset second-order perturbation (MP2) methods. The Si(111) surface was described with Si8H12, Si16H20, and Si22H21 Cluster models. The effect of the basis set superposition error (BSSE) was taken into account by applying the counterpoise (CP) correction. The calculated results indicated that the interactions between the Na+ cation and the dangling bonds of the Si(111) surface are primarily electrostatic with partial orbital interactions. The magnitude of the binding energies depends weakly on the adsorption sites and the size of the clusters. When water molecules are present, the interaction between the Nal and Si(I 11) surfaces weakens and the binding energy has the tendency to saturate. On a Si22H21 cluster described surface, the optimized Na+-surface distance for Na+(H2O)(5) adsorbed at on-top site is 4.16 angstrom and the CP-corrected binding energy (MP2) is -35.4 kJ/mol, implying a weakly adsorption of hydrated Na+ cation on clean Si(111) surface.

Coadsorption of nitric oxide and oxygen on the Ag(110) surface

The coadsorption of NO and O-2 on Ag(110) surface has been studied by X-ray photoelectron spectroscopy (XPS), ultraviolet photoelectron spectroscopy (UPS) and in situ Raman spectroscopy. The existence of oxygen enhances the adsorption of NO by forming the NOx species, that is, NO2 and NO3, and the NO in turn as a promotor facilitates the cleavage of the dioxygen bond, forming the surface atomic oxygen species having the same spectral characteristics as those produced using oxygen at high pressure. The oxygen species generated by the interaction is composed of two parts. One is produced directly by the decomposition of surface NO-O-2 complex at ca 625 K, which raised an O 1s feature at 530.5 eV and is absent at ca 800 K, while the another with an O 1s binding energy of 529.2 eV emerges at higher temperatures and shows similar properties as the reported gamma-state oxygen which bound tightly on restructured silver surface. The exposure to NO and O-2 causes noticeable changes in the morphology of the Ag(110) surface and the flat terraces superseded by small (ca 0.1 mu m) pits, and particles with typical diameters of a few micrometres were formed at elevated temperatures. (C) 1999 Elsevier Science B.V. All rights reserved.

Structure and properties of samarium overlayer and Sm/Rh surface alloy on Rh(100)

The structure and properties of Sm overlayer and Sm/Rh surface alloy have been investigated with Auger electron spectroscopy (AES), low energy electron diffraction (LEED), X-ray photoelectron spectroscopy (XPS), and temperature programmed desorption spectroscopy (TDS). The growth of Sm on Rh(100) at room temperature (RT) appears following the Stranski-Krastanov growth mode and only the trivalent state Sm is observed from XPS results. Thermal treatment of the Sm film at 900 K leads to the formation of ordered surface alloy which shows the c(5 root2 x root2)R45 degrees and c(2 x 2) LEED patterns. Annealing the Sm film at temperature above 400 K makes the binding energy (B.E.) of Sm 3d(5/2) shift to higher energy by 0.7 eV, which indicates charge transfer from Sm to Rh(100) substrate, causing the increase of CO desorption temperature.

Reversible regeneration of molybdenum carbonyl species on an alumina thin film

The thin alumina film-supported metallic molybdenum model catalyst was prepared by thermal decomposition of MO(CO)6, and CO chemisorption on the catalyst was investigated in-situ by thermal desorption spectroscopy (TDS) and X-ray photoelectron spectroscopy (XPS). The results showed that a molybdenum-carbonyl-like species was formed on the alumina surface at low temperature by high coordination of CO with the surface metallic molybdenum nanoparticles, indicating a reversible regeneration of molybdenum carbonyl on the alumina surface. CO chemisorption on the model catalyst surface caused the Mo 3d XPS peak to shift toward higher binding energy. The formed molybdenum carbonyl species appeared at about 240 K in the TDS. The supported metallic molybdenum nanoparticles were quite different from the bulk molybdenum in chemical properties, which indicated a prominent particle-size effect of the clusters.

Study of adsorption of methylene blue and new methylene blue in liquid-solid interface by slab optical waveguide spectroscopy

A slab optical waveguide (SOWG) has been used for study of adsorption of both methylene blue (MB) and new methylene blue (NMB) in liquid-solid interface. Adsorption characteristics of MB and NMB on both bare SOWG and silanized SOWG by octadecyltrichlorosilane (ODS) were compared. Effect of pH on adsorption on MB and NMB was investigated. Binding rate constant analysis showed that both MB and NMB on bare SOWG demonstrates larger association constants than those on ODS-SOWG. Interactions of NIB and NMB on bare SOWG and ODS-SOWG were analyzed by molecular mechanics calculation method. The binding energy change was in the following order: ENMB-bare > EMB-bare > ENMB-ODS > EMB-ODS. (c) 2004 Elsevier B.V. All rights reserved.

Nanoscale electronic properties of conjugated polymers and nanocrystals

The objective of this thesis is the exploration and characterisation of the nanoscale electronic properties of conjugated polymers and nanocrystals. In Chapter 2, the first application of conducting-probe atomic force microscopy (CP-AFM)-based displacement-voltage (z-V) spectroscopy to local measurement of electronic properties of conjugated polymer thin films is reported. Charge injection thresholds along with corresponding single particle gap and exciton binding energies are determined for a poly[2-methoxy-5-(2-ethylhexyloxy)-1,4-phenylenevinylene] thin film. By performing measurements across a grid of locations on the film, a series of exciton binding energy distributions are identified. The variation in measured exciton binding energies is in contrast to the smoothness of the film suggesting that the variation may be attributable to differences in the nano-environment of the polymer molecules within the film at each measurement location. In Chapter 3, the CP-AFM-based z-V spectroscopy method is extended for the first time to local, room temperature measurements of the Coulomb blockade voltage thresholds arising from sequential single electron charging of 28 kDa Au nanocrystal arrays. The fluid-like properties of the nanocrystal arrays enable reproducible formation of nanoscale probe-array-substrate junctions, allowing the influence of background charge on the electronic properties of the array to be identified. CP-AFM also allows complementary topography and phase data to be acquired before and after spectroscopy measurements, enabling comparison of local array morphology with local measurements of the Coulomb blockade thresholds. In Chapter 4, melt-assisted template wetting is applied for the first time to massively parallel fabrication of poly-(3-hexylthiophene) nanowires. The structural characteristics of the wires are first presented. Two-terminal electrical measurements of individual nanowires, utilising a CP-AFM tip as the source electrode, are then used to obtain the intrinsic nanowire resistivity and the total nanowire-electrode contact resistance subsequently allowing single nanowire hole mobility and mean nanowire-electrode barrier height values to be estimated. In Chapter 5, solution-assisted template wetting is used for fabrication of fluorene-dithiophene co-polymer nanowires. The structural characteristics of these wires are also presented. Two-terminal electrical measurements of individual nanowires indicate barrier formation at the nanowire-electrode interfaces and measured resistivity values suggest doping of the nanowires, possibly due to air exposure. The first report of single conjugated polymer nanowires as ultra-miniature photodetectors is presented, with single wire devices yielding external quantum efficiencies ~ 0.1 % and responsivities ~ 0.4 mA/W under monochromatic illumination.

NMR methods for characterizing the pore structures and hydrogen storage properties of microporous carbons.

(1)H NMR spectroscopy is used to investigate a series of microporous activated carbons derived from a poly(ether ether ketone) (PEEK) precursor with varying amounts of burnoff (BO). In particular, properties relevant to hydrogen storage are evaluated such as pore structure, average pore size, uptake, and binding energy. High-pressure NMR with in situ H(2) loading is employed with H(2) pressure ranging from 100 Pa to 10 MPa. An N(2)-cooled cryostat allows for NMR isotherm measurements at both room temperature ( approximately 290 K) and 100 K. Two distinct (1)H NMR peaks appear in the spectra which represent the gaseous H(2) in intergranular pores and the H(2) residing in micropores. The chemical shift of the micropore peak is observed to evolve with changing pressure, the magnitude of this effect being correlated to the amount of BO and therefore the structure. This is attributed to the different pressure dependence of the amount of adsorbed and non-adsorbed molecules within micropores, which experience significantly different chemical shifts due to the strong distance dependence of the ring current effect. In pores with a critical diameter of 1.2 nm or less, no pressure dependence is observed because they are not wide enough to host non-adsorbed molecules; this is the case for samples with less than 35% BO. The largest estimated pore size that can contribute to the micropore peak is estimated to be around 2.4 nm. The total H(2) uptake associated with pores of this size or smaller is evaluated via a calibration of the isotherms, with the highest amount being observed at 59% BO. Two binding energies are present in the micropores, with the lower, more dominant one being on the order of 5 kJ mol(-1) and the higher one ranging from 7 to 9 kJ mol(-1).

Antisense Gene Silencing and Bacteriophages as Novel Disinfection Processes for Engineered Systems

The growth and proliferation of invasive bacteria in engineered systems is an ongoing problem. While there are a variety of physical and chemical processes to remove and inactivate bacterial pathogens, there are many situations in which these tools are no longer effective or appropriate for the treatment of a microbial target. For example, certain strains of bacteria are becoming resistant to commonly used disinfectants, such as chlorine and UV. Additionally, the overuse of antibiotics has contributed to the spread of antibiotic resistance, and there is concern that wastewater treatment processes are contributing to the spread of antibiotic resistant bacteria.

Due to the continually evolving nature of bacteria, it is difficult to develop methods for universal bacterial control in a wide range of engineered systems, as many of our treatment processes are static in nature. Still, invasive bacteria are present in many natural and engineered systems, where the application of broad acting disinfectants is impractical, because their use may inhibit the original desired bioprocesses. Therefore, to better control the growth of treatment resistant bacteria and to address limitations with the current disinfection processes, novel tools that are both specific and adaptable need to be developed and characterized.

In this dissertation, two possible biological disinfection processes were investigated for use in controlling invasive bacteria in engineered systems. First, antisense gene silencing, which is the specific use of oligonucleotides to silence gene expression, was investigated. This work was followed by the investigation of bacteriophages (phages), which are viruses that are specific to bacteria, in engineered systems.


For the antisense gene silencing work, a computational approach was used to quantify the number of off-targets and to determine the effects of off-targets in prokaryotic organisms. For the organisms of Escherichia coli K-12 MG1655 and Mycobacterium tuberculosis H37Rv the mean number of off-targets was found to be 15.0 + 13.2 and 38.2 + 61.4, respectively, which results in a reduction of greater than 90% of the effective oligonucleotide concentration. It was also demonstrated that there was a high variability in the number of off-targets over the length of a gene, but that on average, there was no general gene location that could be targeted to reduce off-targets. Therefore, this analysis needs to be performed for each gene in question. It was also demonstrated that the thermodynamic binding energy between the oligonucleotide and the mRNA accounted for 83% of the variation in the silencing efficiency, compared to the number of off-targets, which explained 43% of the variance of the silencing efficiency. This suggests that optimizing thermodynamic parameters must be prioritized over minimizing the number of off-targets. In conclusion for the antisense work, these results suggest that off-target hybrids can account for a greater than 90% reduction in the concentration of the silencing oligonucleotides, and that the effective concentration can be increased through the rational design of silencing targets by minimizing off-target hybrids.

Regarding the work with phages, the disinfection rates of bacteria in the presence of phages was determined. The disinfection rates of E. coli K12 MG1655 in the presence of coliphage Ec2 ranged up to 2 h-1, and were dependent on both the initial phage and bacterial concentrations. Increasing initial phage concentrations resulted in increasing disinfection rates, and generally, increasing initial bacterial concentrations resulted in increasing disinfection rates. However, disinfection rates were found to plateau at higher bacterial and phage concentrations. A multiple linear regression model was used to predict the disinfection rates as a function of the initial phage and bacterial concentrations, and this model was able to explain 93% of the variance in the disinfection rates. The disinfection rates were also modeled with a particle aggregation model. The results from these model simulations suggested that at lower phage and bacterial concentrations there are not enough collisions to support active disinfection rates, which therefore, limits the conditions and systems where phage based bacterial disinfection is possible. Additionally, the particle aggregation model over predicted the disinfection rates at higher phage and bacterial concentrations of 108 PFU/mL and 108 CFU/mL, suggesting other interactions were occurring at these higher concentrations. Overall, this work highlights the need for the development of alternative models to more accurately describe the dynamics of this system at a variety of phage and bacterial concentrations. Finally, the minimum required hydraulic residence time was calculated for a continuous stirred-tank reactor and a plug flow reactor (PFR) as a function of both the initial phage and bacterial concentrations, which suggested that phage treatment in a PFR is theoretically possible.

In addition to determining disinfection rates, the long-term bacterial growth inhibition potential was determined for a variety of phages with both Gram-negative and Gram-positive bacteria. It was determined, that on average, phages can be used to inhibit bacterial growth for up to 24 h, and that this effect was concentration dependent for various phages at specific time points. Additionally, it was found that a phage cocktail was no more effective at inhibiting bacterial growth over the long-term than the best performing phage in isolation.

Finally, for an industrial application, the use of phages to inhibit invasive Lactobacilli in ethanol fermentations was investigated. It was demonstrated that phage 8014-B2 can achieve a greater than 3-log inactivation of Lactobacillus plantarum during a 48 h fermentation. Additionally, it was shown that phages can be used to protect final product yields and maintain yeast viability. Through modeling the fermentation system with differential equations it was determined that there was a 10 h window in the beginning of the fermentation run, where the addition of phages can be used to protect final product yields, and after 20 h no additional benefit of the phage addition was observed.

In conclusion, this dissertation improved the current methods for designing antisense gene silencing targets for prokaryotic organisms, and characterized phages from an engineering perspective. First, the current design strategy for antisense targets in prokaryotic organisms was improved through the development of an algorithm that minimized the number of off-targets. For the phage work, a framework was developed to predict the disinfection rates in terms of the initial phage and bacterial concentrations. In addition, the long-term bacterial growth inhibition potential of multiple phages was determined for several bacteria. In regard to the phage application, phages were shown to protect both final product yields and yeast concentrations during fermentation. Taken together, this work suggests that the rational design of phage treatment is possible and further work is needed to expand on this foundation.

The Physical and Chemical Structure of Hot Molecular Cores

We have made self-consistent models of the density and temperature profiles of the gas and dust surrounding embedded luminous objects using a detailed radiative transfer model together with observations of the spectral energy distribution of hot molecular cores. Using these profiles we have investigated the hot core chemistry which results when grain mantles are evaporated, taking into account the different binding energies of the mantle molecules, as well a model in which we assume that all molecules are embedded in water ice and have a common binding energy. We find that most of the resulting column densities are consistent with those observed toward the hot core G34.3+0.15 at a time around 10^4 years after central luminous star formation. We have also investigated the dependence of the chemical structure on the density profile which suggests an observational possibility of constraining density profiles from determination of the source sizes of line emission from desorbed molecules.

Positronium scattering by atomic hydrogen with inclusion of target excitation channels

Calculations are reported for positronium (Ps) scattering by atomic hydrogen (H) in the energy range 0-6.5 eV in a coupled- pseudostate approximation in which excitation and ionization channels of both the Ps and the H are taken into account. The approximation contains an accurate representation of the van der Waals coefficient. Results are presented for phase shifts, scattering lengths, effective ranges, and various cross sections including partial wave, total, and ortho-para conversion cross sections. An analysis of the possible spin transitions is provided and the energy of the positronium hydride (PsH) bound state is determined. Substantial differences are found from earlier work within the frozen target approximation, now clearly confirming the importance of target excitation channels. Good agreement is obtained with recent calculations of S-wave phase shifts and scattering lengths using the stabilization method. Convergence to the exact binding energy for PsH appears to be slow. Resonances corresponding to unstable states of the positron orbiting H- are seen in the electronic spin singlet partial waves. The importance of the H- formation channel is discussed.

High harmonic generation by halogen anions and noble gas atoms in a laser field

A comparative study of high harmonic generation (HHG) by atoms and ions with active p-electrons is carried out in the theoretical framework of the rescattering mechanism. The substate with m(l) = 0, i.e. zero orbital momentum projection along the electric vector of a linearly polarized laser wave, is found to give the major contribution to the HHG rate. Our calculations for HHG by an H atom in an excited 2p-state demonstrate that the rate for recombination into a final state with a different value of m(l) (= +/- 1), is higher for lower harmonic orders N, while for higher N (beyond the plateau domain) the difference vanishes. For species with closed electron shells, the m(l)-changing transitions are forbidden by the Pauli exclusion principle. We report absolute HHG rates for halogen ions and noble gas atoms at various intensities. These results demonstrate that the Coulomb binding potential of the atoms considerably enhances both the ionization and recombination steps in the rescattering process. However, the weak binding energy of the anions allows lower orders of HHG to be efficiently produced at relatively low intensities, from which we conclude that observation of HHG by an anion is experimentally feasible.

Application of the zero-range potential model to positron annihilation on molecules

In this paper we use a zero-range potential (ZRP) method to model positron interaction with molecules. This allows us to investigate the e?ect of molecular vibrations on positron–molecule annihilation using the van der Waals dimer Kr2 as an example. We also use the ZRP to explore positron binding to polyatomics and examine the dependence of the binding energy on the size of the molecule for alkanes. We ?nd that a second bound state appears for a molecule with ten carbons, similar to recent experimental evidence for such a state emerging in alkanes with twelve carbons.

Positron-molecule interactions: Resonant attachment, annihilation, and bound states

This article presents an overview of current understanding of the interaction of low-energy positrons with molecules with emphasis on resonances, positron attachment, and annihilation. Measurements of annihilation rates resolved as a function of positron energy reveal the presence of vibrational Feshbach resonances (VFRs) for many polyatomic molecules. These resonances lead to strong enhancement of the annihilation rates. They also provide evidence that positrons bind to many molecular species. A quantitative theory of VFR-mediated attachment to small molecules is presented. It is tested successfully for selected molecule (e.g., methyl halides and methanol) where all modes couple to the positron continuum. Combination and overtone resonances are observed and their role is elucidated. Molecules that do not bind positrons and hence do not exhibit such resonances are discussed. In larger molecules, annihilation rates from VFR far exceed those explicable on the basis of single-mode resonances. These enhancements increase rapidly with the number of vibrational degrees of freedom, approximately as the fourth power of the number of atoms in the molecule. While the details are as yet unclear, intramolecular vibrational energy redistributio (IVR) to states that do not couple directly to the positron continuum appears to be responsible for these enhanced annihilation rates. In connection with IVR, experimental evidence indicates that inelastic positron escape channels are relatively rare. Downshifts of the VFR from the vibrational mode energies, obtained by measuring annihilate rates as a function of incident positron energy, have provided binding energies for 30 species. Their dependence upon molecular parameters and their relationship to positron-atom and positron-molecule binding-energy calculations are discussed. Feshbach resonances and positron binding to molecules are compared with the analogous electron-molecul (negative-ion) cases. The relationship of VFR-mediated annihilation to other phenomena such as Doppler broadening of the gamma-ray annihilation spectra, annihilation of thermalized positrons in gases, and annihilation-induced fragmentation of molecules is discussed. Possible areas for future theoretical and experimental investigation are also discussed.